Objective This study observed the effects of Sishen pills on the pathological characteristics of colon tissue in spleen and kidney yang deficiency ulcerative coliti model rats and expression of PI3K/ Akt / mTOR signaling pathway-related proteins to explore possible mechanisms of inflammation in an ulcerative colon. Methods A total of 120 SPF Wistar rats (half male and half female) were randomly assigned to a blank group of 20, and the other 100 rats were used as the model group. The rat model of ulcerative colitis with spleen-kidney Yang deficiency was established by DNBS / ethanol solution enema + hydrocortisone subcutaneous injection + senna leaf gavage. Rats with successful model establishment were randomly divided into five groups: model, mesalazine, Sishen pill high, Sishen pill medium, and Sishen pill low dose groups. Model and blank groups were administered distilled water. The mesalazine group was orally administered 0. 36 g / kg mesalazine, and the high, middle and low dose groups of Sishen pills were orally administered 3. 2, 1. 6, and 0. 8 g / kg crude drug. Respectively, the volume of which was 10 mL/ kg. Once a day for 21 d, colon tissues of rats were collected to observe general morphology and colon injury. HE staining was used to observe pathological changes. Immunohistochemistry was used to observe the localization and expression levels of PI3K p85, p-PI3K p85, AKT, p-AKT Ser473, mTOR, and p-mTOR Ser2448 proteins in colon tissues. Results Compared with the blank group, the intestinal mucosa had disappeared partially, glands had disappeared, and a large number of inflammatory cells had infiltrated and accumulated in mucosal and basal layers in pathological sections of the model group. The expression of PI3K p85, p-PI3K p85, AKT, p-AKT Ser473, mTOR, and p-mTOR Ser2448 proteins in the model group was increased significantly (P< 0. 01). Compared with the model group, inflammatory cells in the drug groups were reduced, and the structure of the mucosal layer returned to normal to varying degrees. Mesalazine and Sishen pill medium dose groups had the best effects, and the mucosal structure was close to that in the blank control group. Inflammatory cells in the low dose group of Sishen pill were slightly reduced, and a small number of glandular structures was seen. The expression of PI3K p85, p-PI3K p85, AKT, p-AKT Ser473, mTOR, and p-mTOR Ser2448 proteins was decreased to varying degrees in high, middle, low dose groups of Sishen pill and the mesalazine group (P< 0. 01, P< 0. 05). Conclusions Sishen pill may improve intestinal mucosal damage of ulcerative colitis model rats with spleen and kidney yang deficiency by inhibiting activation of the PI3K/ Akt / mTOR signaling pathway.